Contacts of the strand formed by residues 148 - 158 (chain B) in PDB entry 5JSJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140B MET* 4.7 21.8 - - + -
141B PHE 3.4 12.1 - - - +
142B GLU* 4.4 23.6 - - + -
146B GLY 3.5 6.6 + - - +
147B SER* 1.3 79.5 + - - +
149B ASP* 1.3 59.1 + - - +
189B ASP* 6.1 0.9 - - - -
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Residues in contact with ASP 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLU* 4.9 4.5 - - - +
140B MET* 3.7 3.5 - - - +
141B PHE* 3.0 52.9 + - + +
143B THR* 4.7 8.5 - - - +
147B SER* 3.9 2.6 + - - +
148B LYS* 1.3 73.4 - - - +
150B GLU* 1.3 72.7 + - - +
151B TRP* 3.3 21.1 + - - -
172B LYS* 4.4 10.7 + - - -
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLU* 5.2 2.6 - - - +
172A LYS* 4.6 9.4 + - - -
302A MG 4.2 11.8 - - - -
138B GLU* 3.6 34.9 - - + +
139B HIS 3.4 13.7 - - - +
140B MET* 3.3 32.4 - - - +
141B PHE* 4.3 0.2 - - - -
149B ASP* 1.3 84.4 + - - +
151B TRP* 1.3 68.9 + - - +
172B LYS* 4.2 4.0 + - - -
191B ARG* 3.5 27.2 + - - -
302B CL 4.2 4.0 - - - +
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Residues in contact with TRP 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B GLU* 3.6 5.6 - - - -
139B HIS* 2.9 33.6 + - - +
141B PHE* 3.3 30.5 - + + -
149B ASP* 3.3 23.1 + - - -
150B GLU* 1.3 81.2 - - - +
152B ARG* 1.3 62.4 + - - +
153B GLY 3.8 0.9 + - - -
170B TYR* 3.9 31.7 - + + -
172B LYS* 4.1 31.2 - - + +
173B ASP* 3.9 26.9 - - + -
177B TYR* 4.0 5.6 - - - -
301B 6PD 3.3 51.4 - - + -
302B CL 3.8 4.0 - - + -
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Residues in contact with ARG 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A GLU* 6.0 0.4 - - - -
152A ARG* 2.9 41.0 - - - +
171A GLU* 2.8 41.2 + - - -
303A CL 4.2 9.3 - - - +
137B VAL 3.5 2.7 - - - -
138B GLU* 3.4 29.4 + - - +
151B TRP* 1.3 71.9 - - - +
153B GLY* 1.3 58.4 + - - +
170B TYR* 3.4 8.1 - - - +
171B GLU* 3.0 49.0 + - + +
172B LYS 4.8 0.5 + - - -
193B MET* 3.7 31.7 - - + +
302B CL 3.2 17.1 - - + +
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Residues in contact with GLY 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ALA* 3.3 8.5 - - - +
137B VAL* 2.9 39.2 + - - +
151B TRP 3.8 1.4 + - - -
152B ARG* 1.3 76.7 - - - +
154B MET* 1.3 60.8 + - - +
169B THR 3.1 14.4 - - - -
170B TYR* 3.8 8.7 - - - -
171B GLU* 4.7 4.3 + - - +
193B MET* 5.0 0.9 - - - +
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Residues in contact with MET 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B GLY* 3.8 17.9 - - - +
135B LYS 3.4 7.4 - - - +
136B ALA* 4.1 19.5 - - + +
137B VAL* 4.1 1.0 - - - +
153B GLY* 1.3 74.1 - - - +
155B VAL* 1.3 74.8 + - - +
156B LEU* 3.6 17.9 + - + +
168B ILE* 3.3 7.1 - - - +
169B THR* 2.9 38.4 + - + -
239B LYS* 4.0 38.4 - - + +
242B VAL* 5.2 6.1 - - - -
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Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B MET* 3.5 32.1 - - + +
133B ILE* 4.2 11.4 - - + -
134B GLY* 2.8 29.9 + - - -
135B LYS 3.0 5.8 + - - +
137B VAL* 3.8 28.0 - - + -
154B MET* 1.3 76.9 - - - +
156B LEU* 1.3 58.9 + - - +
157B ALA 4.5 0.4 - - - +
166B PHE* 4.2 17.9 - - + -
167B TYR 3.8 11.7 - - - +
168B ILE* 4.4 1.8 - - + -
181B LEU* 3.6 31.0 - - + -
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Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ILE* 3.4 14.9 - - - +
134B GLY* 5.3 0.2 - - - -
154B MET* 3.7 32.3 - - + +
155B VAL* 1.3 75.1 - - - +
157B ALA* 1.3 66.3 + - + +
167B TYR* 3.0 16.9 + - + +
168B ILE 4.2 4.0 - - - +
169B THR* 4.2 16.6 - - + -
176B LEU* 4.0 18.4 - - + -
236B VAL* 3.7 39.0 - - + +
237B GLU 5.5 0.2 + - - -
238B ALA* 3.9 4.4 + - - +
239B LYS* 6.1 1.1 - - + -
242B VAL* 4.6 6.3 - - + -
244B PHE* 3.9 26.5 - - + -
255B VAL* 4.0 17.0 - - + -
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Residues in contact with ALA 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ILE* 3.8 19.7 - - + +
155B VAL* 4.0 0.4 - - - +
156B LEU* 1.3 81.9 - - + +
158B ARG* 1.3 68.3 + - - +
166B PHE* 3.4 6.1 - - - +
167B TYR* 2.7 43.4 + - + +
234B HIS* 6.5 1.3 - - + -
236B VAL* 5.7 1.3 - - + -
237B GLU* 6.5 1.1 - - - -
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Residues in contact with ARG 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ILE* 3.2 40.9 - - - +
126B ALA* 5.5 0.2 - - - +
129B ALA* 3.3 32.2 - - + +
130B ASP* 6.5 0.2 - - - +
133B ILE* 3.8 9.1 - - + +
157B ALA* 1.3 81.7 - - - +
159B ALA* 1.3 69.2 + - - +
160B PRO* 3.6 4.9 - - - +
163B ASN* 2.7 41.5 + - - +
164B THR* 4.4 0.2 - - - +
165B TRP 3.8 5.8 - - - +
166B PHE* 3.8 19.0 - - + -
167B TYR* 4.7 1.4 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il